I can't diagnose your Fluxbox problem, at least not without more info, but as to the backup file:
Many Linux text editors, when you edit a file (foo) leave an original copy with the same file name but a tilde appended to it (foo~). This is not necessarily default behavior with every editor on every distro.
What I've taken to doing when I'm making line by line edits in files such as .xintrc is remarking out the old lines with a number sign at the beginning of them, then writing the new line(s). That makes it very easy to drop back.
In my own .xinitrc one on of my machines, I have calls for three different window managers/desktop environments. I change among them by moving the number signs around.
For your Fluxbox, try starting it from the command line with "fluxbox," "exec fluxbox," and "exec startfluxbox." Make a note of any error messages that appear in the terminal (a digital camera may be a help here, but there are ways to take a screenshot from a terminal